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MSGFplus

An interface between R and MS-GF+

This package contains function to perform peptide identification using the MS-GF+ algorithm. The package contains functionality for building up a parameter set both in code and through a simple GUI, as well as running the algorithm in batches, potentially asynchronously.

Functions (33)

MSGFplus-package

An interface between R and MS-GF+

chargeRange

Get and set the charge range in msgfPar objects

Get and set database in msgfPar objects

Get and set enzyme in msgfPar objects

fragmentation

Get and set fragmentation in msgfPar objects

Get a string representation of an msgfPar-related object

Get and set instrument in msgfPar objects

isotopeError

Get and set isotope error in msgfPar objects

lengthRange

Get and set peptide length range in msgfPar objects

Get and set the number of matches in msgfPar objects

mods

Get and set the modifications in msgfPar objects

msgfAsync-class

A class referencing an asynchronous execution of MS-GF+

Constructor for the msgfPar class

msgfPar-class

A class to contain parameters used in an MS-GF+ analysis

msgfParChargeRange-class

A class handling charge ranges

msgfParEnzyme-class

A class handling enzyme selection

msgfParFragmentation-class

A class handling Fragmentation types

msgfParFromID

Extract parameters from mzIdentML result file

msgfParInstrument-class

A class handling instrument types

msgfParIsotopeError-class

A class handling isotope errors

msgfParLengthRange-class

A class handling length ranges

msgfParMatches-class

A class handling number of matches

msgfParModification-class

A class handling modification characteristics

msgfParModificationList-class

A class handling a list of modifications

msgfParNtt-class

A class handling cleavage specificity

msgfParProtocol-class

A class handling protocol choice

msgfParTda-class

A class handling use of target-decoy approach for FDR estimation

msgfParTolerance-class

A class handling parent ion tolerance

ntt

Get and set cleavage specificity in msgfPar objects

Get and set protocol in msgfPar objects

Runs MS-GF+ based on the given msgfPar object

tda

Get and set use of target-decoy approach in msgfPar objects

Get and set the parent tolerance in msgfPar objects

MSGFplus

An interface between R and MS-GF+

v1.24.0

GPL (>= 2)

Authors

Thomas Lin Pedersen

Initial release

2020-09-01

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